Increasing agricultural land use and intensification have given rise to the loss and eutrophication of coastal wetlands worldwide. In Mediterranean coastal regions, irrigated agriculture, in turn, has prompted the proliferation of farm ponds which might compensate for wetland loss and degradation if their management regimen results are compatible with biodiversity conservation. Here, we studied regional (γ-), local (α-) and interlocal (β-) diversities of chironomids in coastal wetlands and irrigation ponds from a Mediterranean region, to determine the contribution of each habitat type to regional diversity, and to disentangle which environmental factors, anthropogenic or natural, contributed most to explain diversity patterns. Regional diversity was slightly, but still significantly, higher in natural wetlands than in farm ponds, which can be attributed to the significantly higher β-diversity in natural wetlands, since, despite the much larger surface area of wetlands, both habitat types did not differ in local diversity (α-diversity). In both habitats, however, the contribution of β-diversity to regional diversity was higher compared to that of α-diversity, and the component ‘spatial species turnover’ exceeded that of the component ‘nestedness’ of β-diversity. This, together with an outstanding assemblage complementarity (approx. 50%) between habitat types, emphasizes the vital contribution of farm ponds, together with natural wetlands, to regional diversity. Despite the higher salinity and eutrophication of natural wetlands that tended to reduce diversity in chironomid assemblages, their more heterogeneous shore line likely compensated somewhat for such negative effects. Unlike wetlands, the homogeneous and unvegetated shore of farm ponds, in conjunction with their intensive management, probably induced adverse effects on local and interlocal diversity. Specific recommendations are given in this regards to mitigate impacts and improve the value of both habitats for biodiversity conservation.